[R-pkg-devel] Vignette does not show up after loading package

Rik Verdonck Rik.Verdonck at bio.kuleuven.be
Wed Jun 3 18:16:16 CEST 2015

Hi all,

I am developing a package for the interpretation of mass spectrometry data, which can be found here: https://github.com/goat-anti-rabbit/labelpepmatch.R

I wrote a vignette that compiles fine into a .html using knitr in Rstudio.
The output line in the vignette.rmd file looks like :

??output: rmarkdown::html_vignette

However, when I use devtools::install_github("goat-anti-rabbit/labelpepmatch.R") or devtools::install_github("goat-anti-rabbit/labelpepmatch.R",build_vignettes = TRUE), the package loads normally, but no vignette is found when using browseVignettes("labelpepmatch") or vignette("labelpepmatch").

I don't really get this, because as far as I understood, shouldn't the package be able to build the vignette from scratch?

I also tried with these lines for output:

    theme: readable
    highlight: default
    toc: yes

And it nicely knits into example html and pdf files, but no real files are created in the labelpepmatch/vignettes directory. Any suggestions here?

So: recap of my questions:
1. Should it be possible for the vignette to be built from scratch and if yes, what is missing in my package for this functionality to work?
2. How can I make knitr output a html AND pdf in my vignettes directory?

Looking forward to your replies.
Many, many thanks!

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